A new single nucleotide polymorphism in the chicken pituitary-specific transcription factor (POU1F1) gene associated with growth rate

2004 ◽  
Vol 35 (4) ◽  
pp. 344-346 ◽  
Author(s):  
R. Jiang ◽  
J. Li ◽  
L. Qu ◽  
H. Li ◽  
N. Yang
Keyword(s):  
Growth Rate ◽  
Single Nucleotide Polymorphism ◽  
Transcription Factor ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Pou1f1 Gene ◽  
Specific Transcription Factor

scholarly journals A novel single nucleotide polymorphism of the POU1F1 gene associated with meat quality traits in rabbits

2015 ◽  
Vol 15 (3) ◽  
pp. 611-620 ◽  
Author(s):  
Jie Wang ◽  
Guowu Li ◽  
Mauricio A. Elzo ◽  
Linjun Yan ◽  
Shiyi Chen ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Meat Quality ◽  
Biceps Femoris ◽  
Quality Traits ◽  
Nucleotide Polymorphism ◽  
Chi Square ◽  
Single Nucleotide ◽  
Pou1f1 Gene ◽  
Biceps Femoris Muscle ◽  
Meat Quality Traits

Abstract The purpose of this research was to investigate the effect of the POU1F1 gene on meat quality traits in the Hyla, Champagne, and Tianfu Black rabbit breeds. We detected one single nucleotide polymorphism and the SNP was located at 536 bp in intron 5 of this gene. Chi-square tests showed that the genotypic frequencies in the three rabbit populations were not in Hardy-Weinberg equilibrium. The PIC values indicated that the three populations had intermediate levels of genetic diversity. Rabbits with the CC genotype had a significantly greater pH0h than those with the CT genotype in the biceps femoris muscle. The least squares means for cooking loss in CT and CC rabbits were significantly higher than those for TT rabbits. Rabbits with the CC genotype had a significantly higher intramuscular fat content in the longissimus dorsi and biceps femoris muscles than those with genotype TT and CT. Thus, the results here indicate that this POU1F1 SNP may be of potential use in marker assisted selection for meat quality traits in rabbits.

A Single Nucleotide Polymorphism in an R2R3 MYB Transcription Factor Triggers ms6 (Ames1) Male Sterility in Soybean

2021 ◽  
Author(s):  
Junping Yu ◽  
Guolong Zhao ◽  
Wei Li ◽  
Ying Zhang ◽  
Peng Wang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Transcription Factor ◽  
Male Sterility ◽  
Anther Development ◽  
Hybrid Breeding ◽  
Myb Transcription Factor ◽  
Hybrid Seed Production ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
R2r3 Myb

Abstract Soybean [Glycine max (L.) Merr.] is an important crop providing vegetable oils and proteins. Increasing demand on soy products heightens the urgency of soybean yield improvement. Hybrid breeding with male sterility system is an effective method to improve crop production. Cloning of genic male sterile (GMS) gene combined with biotechnology method can contribute to constructing GMS-based hybrid Seed Production Technology (SPT) to promote soybean performance and yield. In this research, we identified a soybean GMS locus, GmMS6, by combining bulked segregant analysis (BSA)-sequencing and map-based cloning technology. GmMS6 encodes an R2R3 MYB transcription factor, whose mutant allele in ms6 (Ames1) harbors a single nucleotide polymorphism (SNP) substitution, leading to the 76th Leucine to Histidine change in the DNA binding domain. Phylogenetic analysis demonstrates GmMS6 is a homolog of Tapetal Development and Function 1 (TDF1)/MYB35 that is an anther development key factor co-evolved with angiosperm. It has a recently duplicated homolog GmMS6LIKE (GmMS6L), both of which can rescue the male fertility of Arabidopsis homologous mutant attdf1 while GmMS6L76H cannot, denoting that both proteins are functional and L76 is a critical residue for TDF1’s function. However, compared to anther specific expressed GmMS6, GmMS6L is constitutively expressed at a very low level, explaining deficiency of GmMS6 alone causes pollen abortion. Moreover, the expression levels of major regulatory and structural genes for anther development are significantly decreased in ms6, unveiling that GmMS6 is a core transcription factor regulating soybean anther development.

scholarly journals A Single Nucleotide Polymorphism Uncovers a Novel Function for the Transcription Factor Ace2 during Candida albicans Hyphal Development

PLoS Genetics ◽  
2015 ◽  
Vol 11 (4) ◽  
pp. e1005152 ◽  
Author(s):  
Diana M. Calderón-Noreña ◽  
Alberto González-Novo ◽  
Sara Orellana-Muñoz ◽  
Pilar Gutiérrez-Escribano ◽  
Yolanda Arnáiz-Pita ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Transcription Factor ◽  
Candida Albicans ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Hyphal Development

scholarly journals Identification of Deleterious Single Nucleotide Polymorphism (SNP)s in the Human TBX5 Gene & Prediction of Their Structural & Functional Consequences: An In Silico approach

2020 ◽  
Author(s):  
A M U B Mahfuz ◽  
Md. Arif Khan
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Transcription Factor ◽  
In Silico ◽  
Developmental Process ◽  
Upper Limbs ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Functional Consequences ◽  
Tbx5 Gene

ABSTRACTT-box transcription factor 5 (TBX5) gene encodes the transcription factor TBX5 which plays a crucial role in the development of the heart and upper limbs. Alternative splicing resulting in several isoforms regulate the functions of this gene during the developmental process. Damaging single nucleotide variants in this gene alter the structure and disturb the functions of TBX5 and ultimately cause Holt-Oram Syndrome (HOS), an autosomal dominant disease where various congenital malformations of the heart (with or without conduction defects), upper limbs and shoulder girdles are observed. Besides HOS, TBX5 single nucleotide variants can also be associated with Dilated Cardiomyopathy, Atrial Fibrillation, and Tetralogy of Fallot without skeletal deformity.By exploiting available Single Nucleotide Polymorphism information in dbSNP, this study was designed to identify in silico the deleterious TBX5 SNPs, and predict their structural and functional consequences, and alteration of biochemical properties on the candidate protein. For this purpose, various reliable in silico analysis tools such as PROVEAN, SIFT, PolyPhen-2, MutPred2, PredictSNP1, PredictSNP2, MetaLR, MetaSVM, REVEL, ConSurf, NetsurfP-2.0, iStable 2.0, Missense3D, UTRdb, MirSNP, and Human Splicing Finder (HSF) have been used. 58 missense substitutions were found damaging by both sequence homology-based tools SIFT (Sorting Intolerant from Tolerant) and PROVEAN (Protein Variation Effect Analyzer), and structure homology-based tool PolyPhen-2 (Polymorphism Phenotyping-2). Among these 58 substitutions, 13 are already annotated as Pathogenic/Likely Pathogenic in ClinVar database, and so they were excluded. Then, the rest 45 high confidence substitutions were further scrutinized by various disease association predicting meta servers. Next, conservation profile of the native amino acid residues, their surface & solvent accessibility, and stability and structural integrity of the protein upon mutation were assessed. Analysis of 1 stop loss SNP, and 2 nonsense SNPs were done by PredictSNP2. Analysis of SNPs in the UTR region were done using UTRdb and MirSNP, and splice site SNPs were evaluated by Human Splicing Finder (HSF). This study provides a comprehensive list of most deleterious SNPs onTBX5 gene. The results from this study can help in early diagnosis of HOS and in relevant genetic counseling.

G125A Single Nucleotide Polymorphism (SNP) in 5′-UTR of the Tumor Suppressor Gene Bax Affects Its Transcriptional Regulation.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2250-2250
Author(s):  
Anurag Saxena ◽  
Keith Bonham ◽  
Evan Neuls ◽  
Oksana Moshynska
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Luciferase Reporter ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Major Band ◽  
Bax Protein ◽  
Gene Assay ◽  
Competition Assays

Abstract Lower expression of Bax protein in various human malignancies is associated with poor response to treatment and shorter disease-free survival. We (Cancer Lett2002; 187:199–205) and others (J Clin Oncol; 23:1514–21) have shown the association of a single nucleotide polymorphism (SNP) in the BAX promoter (G125A) with reduced protein expression and treatment resistance in chronic lymphocytic leukemia (CLL). Using luciferase reporter gene assay we demonstrated that this SNP significantly reduced BAX promoter activity (Oncogene2005; 24:2042–9). Our aim was to determine the effect of this polymorphism on the binding of transcription factors. For electrophoretic mobility shift (EMSA), HeLa and K562 nuclear extracts, and for chromatin immunoprecipitation (ChIP), K562 cells were used to study their ability to bind to a radiolabeled DNA probe corresponding to the BAX promoter region with G nucleotide at the position 125 or bearing G125A SNP. Super-shift assay was performed to determine the transcription factor involved in binding. Competition assays were performed to determine differences in the binding ability of the two probes. A panel of antibodies was tested by super-shift and ChIP assays, non-specific antibodies served as negative controls. Two major band shifts were detected by EMSA. The mobility of the detected complexes was different from those observed with GC1 probe, specific for Sp1/Sp3, suggesting the involvement of transcription factors other than Sp1/ Sp3. This was confirmed in super-shift assay and ChIP assay by incubating DNA probes with Sp1 or/ and Sp3 antibodies. We also found in the competition assays that the cold probes competed differently for binding. The findings provide evidence of the ability of G125A SNP to influence transcription factor binding in vitro (as shown in EMSA experiments) and in vivo (in ChIP experiments).

scholarly journals Familial X-Linked Acrogigantism: Postnatal Outcomes and Tumor Pathology in a Prenatally Diagnosed Infant and His Mother

2019 ◽  
Vol 104 (10) ◽  
pp. 4667-4675 ◽  
Author(s):  
Brittany K Wise-Oringer ◽  
George J Zanazzi ◽  
Rebecca J Gordon ◽  
Sharon L Wardlaw ◽  
Christopher William ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Pituitary Adenoma ◽  
Tumor Cells ◽  
Chorionic Villus ◽  
Proliferation Index ◽  
Stem Cell Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Abstract Context X-linked acrogigantism (X-LAG), a condition of infant-onset acrogigantism marked by elevated GH, IGF-1, and prolactin (PRL), is extremely rare. Thirty-three cases, including three kindreds, have been reported. These patients have pituitary adenomas that are thought to be mixed lactotrophs and somatotrophs. Case Description The patient’s mother, diagnosed with acrogigantism at 21 months, underwent pituitary tumor excision at 24 months. For more than 30 years, stable PRL, GH, and IGF-1 concentrations and serial imaging studies indicated no tumor recurrence. During preconception planning, X-LAG was diagnosed: single-nucleotide polymorphism microarray showed chromosome Xq26.3 microduplication. After conception, single-nucleotide polymorphism microarray on a chorionic villus sample showed the same microduplication in the fetus, confirming familial X-LAG. The infant grew rapidly with rising PRL, GH, and IGF-1 concentrations and an enlarging suprasellar pituitary mass, despite treatment with bromocriptine. At 15 months, he underwent tumor resection. The pituitary adenoma resembled the mother’s pituitary adenoma, with tumor cells arranged in trabeculae and glandular structures. In both cases, many tumor cells expressed PRL, GH, and pituitary-specific transcription factor-1. Furthermore, the tumor expressed other lineage-specific transcription factors, as well as SOX2 and octamer-binding transcription factor 4, demonstrating the multipotentiality of X-LAG tumors. Both showed an elevated Ki-67 proliferation index, 5.6% in the mother and 8.5% in the infant, the highest reported in X-LAG. Conclusions This is a prenatally diagnosed case of X-LAG. Clinical follow-up and biochemical evaluation have provided insight into the natural history of this disease. Expression of stem cell markers and several cell lineage-specific transcription factors suggests that these tumors are multipotential.

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